Wishing You Were Somehow Here Again -- POTO
Castle on a Cloud -- Les Miz
Not a Whole Song, but the one line reprise from MOTN to end the show -- "It's over now, the Music of the Night." -- POTO
Phantom Faces at the Window -- Les Miz
The one about innocents going off to war (to the tune of "Lovely Ladies") -- Les Miz
Anatevka Reprise when everyone is leaving the town -- Fiddler on the Roof
Edelweiss -- Sound of Music (because everyone in retrospect knows what the Anschluss started)
If/Then -- almost everything towards the end of the married with children timeline, from "I Hate You" on.
Note: It's the heartbreak in the middle of Les Miz that makes it so hard for me to watch, including "On My Own," which others have mentioned.
Audrey, the Phantom Phanatic, who nonetheless would rather be Jean Valjean, who knew how to make lemonade out of lemons.